SIMcheck Manual
===============

SIMcheck is a package of ImageJ tools for assessing the quality and reliability
of Structured Illumination Microscopy (SIM) data. Although originally developed
for GE Healthcare OMX data, SIMcheck may be used with data from other systems
including Zeiss's ELYRA and Nikon's N-SIM. It should work with any fairly
recent ImageJ version, and can be installed by copying the ``SIMcheck_.jar``
file into your plugins folder and restarting ImageJ. 

.. image:: images/SIMcheck_logo.jpg
    :width: 250px
    :align: right
    :alt: SIMcheck logo

Please read the :ref:`quick-start` guide below.

Contents:

.. toctree::
   :maxdepth: 2

   quickstart
   raw_data_checks
   rec_data_checks
   cal_checks
   utils
   theory_gloss
   SI_systems
   developer


Indices and tables
==================

* :ref:`genindex`
* :ref:`search`